Download OBIS-SEAMAP data

General

OBIS-SEAMAP provides flexible and powerful data download features. The observation records and effort / telemetry tracks can be downloaded as a CSV or an ESRI file geodatabase / shapefile. You can download all the observation records of a dataset or a species. Moreover, you can set criteria and download the data that meet the criteria (e.g. multiple species from parrticular datasets in your study area).

Data follow the standardized OBIS-SEAMAP schema and not from the data originally provided by data providers. They include publicly available or minimum fields: locations (latitude and longitude in decimal degrees), date/time of the observations, the species identification and group size. For a telemetry or photo-id dataset, animal or device id is included. See below for more details about the fields.

Also see "FAQ" at the bottom of the page.

Data sharing policy

Please observe the data sharing policy and follow the Terms of Use. The data sharing policy is set per dataset. You are not allowed to download the dataset under "permission required" option unless you have gotten permission from the data provider. Please note that records from datasets under "permission required" policy will show up on the maps on the OBIS-SEAMAP mapping tools but not be included in the download file. The data sharing policy per dataset is summarized in the datasets_and_citations.csv file included in the zipped file.

OBIS-SEAMAP adopts Creative Commons licenses and adds the "permission required" option.

  Permission Attribution Commercial use Attributes
CC0 Not required No but strongly suggested Yes All
CC BY Not required Yes Yes Minimum or All
CC BY-NC Not required Yes No Minimum or All
Permission required Required Yes - -

The data sharing policy of the dataset is found in the "Sharing policy" in the metadata section of the Dataset Page.

The sharing policy is also shown in the Datasets on Map sub panel which opens up when the number in line with Datasets in the Map Summary panel is clicked.

How to download

  1. Find the dataset or species you are interested in and visit the Species Profile Page or Dataset Page. If you are interested in multiple species or datasets, visit the Advanced Search.
  2. Set up criteria and make sure the map shows the data you are interested in or move to the next step without setting up criteria if you want to download the whole data for a species or a dataset.
  3. Click [Download] icon in the icon tray at the left side of the window.
    Note: [Download] icon is disabled for the dataset under "permission required" policy.
  4. Read OBIS-SEAMAP Terms of Use and agree to it by clicking [Agree]. Otherwise, click [Cancel] to close the download wizard window. If you don't agree on the Terms of Use, you can't download the data.
  5. In the second wizard panel, fill in the [First / Last name], [Affiliation], [E-Mail], [Intended use of data] boxes. All fields are required.

    The information provided here helps us trace the usage of the OBIS-SEAMAP database and recognize your research goals. The OBIS-SEAMAP team members may contact you to better understand your purpose of the data download.

    The information will be stored in our database but not be used to other porposes than the management of OBIS-SEAMAP.
  6. Once all the boxes are filled, click [Next].
  7. In the third and final wizard panel, choose what kind of data set you want to download.

    On the Advanced Search, [Data on Map Currently Visible] is the only option available. This option extracts data you see currently on the map reflecting the criteria you set up though those from datasets under "permission required" are excluded.

    On the Dataset Page, [Complete Set of Dataset] is also available. This option downloads a prepared set of data including observation records and tracks if available. This option does not take in any criteria currently set.

    On the Species Profile Page, [All Species Observations] is also available. This option downloads a prepared set of observation records of the species. This option does not take in any criteria currently set. Note that a set of observation records will grow as new datasets are added that observed the species of interest. Therefore, writing down the date you downloaded the data is useful. Also note that records from datasets under "permission required" are excluded.
  8. Select one of the download formats. What are included in the download zip file are slightly different among the formats. See the table below.
    Supported formats are:
    • Comma-separated values (CSV; .csv)
    • ESRI File Geodatabase (.gdb) or Shapefile (.shp): Currently, "Complete Set of Dataset" is provided in File Geodatabase. "All Species Observations" and "Data on Map Currently Visible" are provided in shapefile. It is planned that "All Species Observations" will be provided in file geodatabase.
    • Google Earth KML (.kml)
    • OGC WFS (.xml)
    • OGC WMS (.png)
    A click on the data format button starts the download process. It may take several minutes to prepare the download data. You see the progress in the status box below the format buttons.
  9. When the browser's save dialog appears, select the folder you want to save it in. Data in any format except WMS are zipped. A WMS image will open up in a new browser tab/window.
  10. Unzip the downloaded file.

What included

The zipped download file includes the following files depending on the type (platform) of the dataset, data selection option and the page you download the data on (i.e. Dataset Page, Species Page or Advannced Search).

Data Selection Complete Set of Dataset All Species Observations Data on Map Currently Visible
Data type  Observation
(boat, plane)
Telemetry
(tag)
Mix Mix
Point observations Yes No Yes Yes, if the Points layer is on.
Point telemetry location No Yes Yes, if exists Yes, if exists
Ship/plane effort lines Yes, if available No No No
Animal track lines No Yes, if available No No
Gridded summary No No No Yes, if the Summary layer is on.
Datasets and citations info* **
Yes
Yes
Yes
Formats available
CSV / ESRI File Geodatabase / KML
(WFS / WMS)****
CSV / ESRI File Geodatabase / KML
(WFS / WMS)****
CSV / ESRI Shapefile / KML
WFS / WMS
FGDC metadata*
Yes
Yes Yes
Terms of Use*
Yes
Yes Yes
File name* *** dataset_[dataset_id]_points_[format]
species_[tsn]_points_[format]
custom_[request_id]_[type]_[format]

*The information is not included for KML and WMS formats.

**Datasets and citations info

The information on datasets that provided the data you downloaded is listed in the CSV file. The actual file name follows the rule:

obis_seamap_[download type]_[id]_datasets_and_citations.csv

where [download type] is "dataset", "species", or "custom" according to the Data Selection options "Dataset on Dataset Page", "Species on Species Profile Page" and "Data on map", respectively.

The informatoin includes dataset name, provider's contact information, data sharing policy and citation to the dataset as well as the link to the online metadata (XML format) for the dataset. The CSV file should include only one record when you downloaded the data with "Dataset on Dataset Page" option.

When you use the downloaded data for your research that leads to publicly available product or publication, you are required to give credit to all datasets/providers that provided data you downloaded. We suggest you use the citation in the CSV file.

***File name

  • All file names have a prefix "obis_seamap_".
  • [format] indicates the format you chose: "csv", "shapefile", "gdb" or "wfs".
  • [dataset_id] indicates the Dataset ID, which you can see 'OBIS-SEAMAP ID' row in the Dataset Page (effort or telemetry track lines has a different ID) as well as [dataset_id] field in the CSV / shapefile.
  • [tsn] indicates the taxonomic serial number (TSN) of the species.
  • [request_id] indicates an unique ID assigned by the system per download request.
  • [type] indicates the layer selection option you chose: "points", "dist_sp_xxxdeg" or "dist_taxa_xxxdeg" where xxx is the resolution (1, 01 or 001).

****WFS / WMS

WFS and WMS formats are not selectable for the Quick Download that is available on the Front Page.

FGDC metadata

The FGDC-compliant metadata in XML format for all the datasets that provided the data you downloaded are placed in the "fgdc_metadata" folder in the zipped download file. It is very helpful to take a look at the metadata for proper use of the data for your analyses. The datasets and citations info file (CSV) includes the links to the local or online metadata so that you can quickly find the metadata for the dataset you are interested in. Note that there should be only one metadata in the fgdc_metadata folder when you downloaded the data with "Dataset on Dataset Page" option.

CSV / File Geodatabase (or Shapefile) field definitions

Observation and telemetry point data

The CSV and file geodatabase (shapefile) have the same field definitions. Ignore [Type] for CSV.

Field Type Description
dataset_id Long integer Dataset ID.
row_id Text Row id unique among the OBIS-SEAMAP database.
latitude Double Latitude of the point in decimal degrees.
longitude Double Longitude of the point in decimal degrees.
sp_code Text Species code that the data provider used to identify the species.
scientific Text Species scientific name.
common Text Species English common name, if any.
tsn Long integer Taxonomic Serial Number for the species organized by Integrated Taxonomic Information System.
count Long integer Number of animals observed at the sighting. May have different definition, count methods. Contact the data provider for more detail. This is always 1 (one) for telemetry data.
series_id Text Identification of the animal. For telemetry or PhotoID data only.
obs_date Date Date of the observation. Time is not included.
date_time Text Date and time of the observation in "yyyy-mm-dd hh:mm:ss" format.
Note: An ESRI shapefile can not contain both date and time in a Date type field.
last_mod Text Date and time the data was last modified. Note that the data may be updated due to error correction or other reasons.
provider Text The institution name of the data provider.
owner Text The data provider expressed as an OBIS-SEAMAP user account.
oceano Text Remote sensed oceanographic data sampled againt the observation location and date.
depth Double The depth of the observation, if available.
ds_type Text Data type.

Effort and animal track lines

Ship/plane effort line and animal track line data have the same field definitions.

Field Type Description
dataset_id Long integer Dataset ID seen in 'Effort'/'Trackline' row in Dataset page. This is different from that for the related observation/telemetry dataset.
row_id Text Row id unique in the OBIS-SEAMAP database.
series_id Text Identification of the animal for telemetry data.
lon_s Double Longitude of the beginning point of the line segment in decimal degrees.
lat_s Double Latitude of the beginning point of the line segment in decimal degrees.
lon_e Double Longitude of the end point of the line segment in decimal degrees.
lat_e Double Latitude of the end point of the line segment in decimal degrees.
date_s Date Date of the beginning point of the line segment.
date_e Date Date of the end point of the line segment.
datetime_s Text Date and time of the beginning point of the line segment.
datetime_e Text Date and time of the end point of the line segment.
length_km Double The length of the segment in km.
speed_kph Double Averaged speed in km/h at which the ship/plane/animal travels along the line segment.
eff_status Text Effort status (on or off) for ship/aerial surveys, if available.
ds_type Text Data type.

Summary data

The CSV and shapefile have the same field definitions.

Field Type Description
CSV
Shapefile
oid / FID Integer Unique ID for row
Y (oid)
Y (FID)
longitude Double Longitude of the centroid of the cell in decimal degrees.
Y
Y
latitude Double Latitude of the centroid of the cell in decimal degrees
Y
Y
providers Text Provider names, separated with ";"
Y
N
species Text Species scientific name, separated with ";"
Y
Y
datasets Text Dataset IDs, separated with ";"
Y
Y (dataset)
date_min Text Minimum date of the records in the cell.
Y
Y
date_max Text Maximum date of the records in the cell.
Y
Y
num_records Integer The number of records that fall in the cell.
Y
Y (num_record)
num_animals Integer The sum of the group size in the cell.
Y
Y (num_animal)
num_species Integer The number of species in the cell.
Y
Y (num_sp)
csquare Text String expression of the cell.
Y
Y
geom_wkt Text Well known text representation of the cell.
Y
Y
shannon Double Shannon diversity index (included on dist_taxa mode)
Y
Y
simpson Double Simpson diversity index (included on dist_taxa mode)
Y
Y
hurlberts Double Hurlbert's diversity index (included on dist_taxa mode)
Y
Y

*dist_taxa mode: dist_taxa mode is visualized when no dataset or species is set as a criterion.

Download FAQ

I'm exploring the data with Advanced Search and want to download a full set of records of a particular dataset. How can I do that?
The download wizard on the Advanced Search makes downloadable the data currently on the map. That means some records of a dataset may be filtered out in the download file under the current criteria.
To download a full set of records of a dataset, open the Datasets Panel that lists all the datasets currently visible. At the far right in each row is the download icon that allows you to download the full set of the dataset. Alternatively, you can go to the Dataset Page by clicking the title of the dataset.
I know the dataset has effort data but I can't download it. How can I download effort data?
The effort data is included in the downloadable zipped file for a dataset. You have to choose [Complete Set of Dataset] option for the data type. This option is not available on the Advanced Search, so you should go to the Dataset Page.
I don't see the effort feature class in the zipped file?
Not all the datasets have effort data. You can see if the dataset has effort data in the dataset metadata on the Dataset Page or Datasets tab in the Data Panel.
What are the advantages of ESRI file geodatabase over shapefile?
In OBIS-SEAMAP ver. 4, ESRI file geodatabase has become one of the supported data format, replacing shapefile format for the "Complete Set of Dataset" and "All Species Observations". There are a couple of advantages of file geodatabase over shapefile.
  • The limit of the field name length is eased in file geodatabase with 64 characters allowed. It it 10 characters in shapefile.
  • The date type in file geodatabase can contain both date and time whereas shapefile's date field can't.
  • The text data in shapefile is up to 254 characters while file geodatabase has virtually no limit.
Please note that download option "Data on Map" still uses shapefile format.
Why is [date_time] field of text type?
The database that ESRI shapefile is based on (DBF) does not support Time type and a Date type field cannot hold time part due to the field size limit. Thus, we decided to hold date and time values in a text field. The date part is also available in [obs_date] field that is date type.

Note that this limitation is eased in ESRI file geodatabase. In the feature class in a file geodatabase, the date and time is placed in [date_time], which is a date type field.
I want to sort the attribute table by date/time. How can I do it?
Since [date_time] field in a shapefile is written in a format appropriate for sorting, the sorting on date/time will work fine even though it's a text type field.

1. Open the attribute table (in ArcMap or ArcCatalog).
2. Select the [date_time] field.
3. Keeping it highlighted, right-click and select 'Sort Ascending/Descending'.
sort by date
 
How do I use oceanographic sampled data in [oceano] field?
See "Download Sampled Values and Utilize Them" in the Oceanographic Variables available on Mapping Tool page.
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